The Potential for SARS-CoV-2 to Evade Both Natural and Vaccine-induced Immunity

Mapping Intimacies ◽

10.1101/2020.12.13.422567 ◽

2020 ◽

Cited By ~ 1

Author(s):

Emily Shang ◽

Paul Axelsen

Keyword(s):

Human Infection ◽

Antibody Binding ◽

Spike Protein ◽

Wild Type ◽

Binding Interface ◽

Naturally Occurring ◽

Binding Interfaces ◽

Induced Immunity ◽

Wild Type Form

SARS-CoV-2 attaches to the surface of susceptible cells through extensive interactions between the receptor binding domain (RBD) of its spike protein and angiotensin converting enzyme type 2 (ACE2) anchored in cell membranes. To investigate whether naturally occurring mutations in the spike protein are able to prevent antibody binding, yet while maintaining the ability to bind ACE2 and viral infectivity, mutations in the spike protein identified in cases of human infection were mapped to the crystallographically-determined interfaces between the spike protein and ACE2 (PDB entry 6M0J), antibody CC12.1 (PDB entry 6XC2), and antibody P2B-2F6 (PDB entry 7BWJ). Both antibody binding interfaces partially overlap with the ACE2 binding interface. Among 16 mutations that map to the RBD:CC12.1 interface, 11 are likely to disrupt CC12.1 binding but not ACE2 binding. Among 12 mutations that map to the RBD:P2B-2F6 interface, 8 are likely to disrupt P2B-2F6 binding but not ACE2 binding. As expected, none of the mutations observed to date appear likely to disrupt the RBD:ACE2 interface. We conclude that SARS-CoV-2 with mutated forms of the spike protein may retain the ability to bind ACE2 while evading recognition by antibodies that arise in response to the original wild-type form of the spike protein. It seems likely that immune evasion will be possible regardless of whether the spike protein was encountered in the form of infectious virus, or as the immunogen in a vaccine. Therefore, it also seems likely that reinfection with a variant strain of SARS-CoV-2 may occur among people who recover from Covid-19, and that vaccines with the ability to generate antibodies against multiple variant forms of the spike protein will be necessary to protect against variant forms of SARS-CoV-2 that are already circulating in the human population.

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Age-Dependent Reduction in Neutralization against Alpha and Beta Variants of BNT162b2 SARS-CoV-2 Vaccine-Induced Immunity

Microbiology Spectrum ◽

10.1128/spectrum.00561-21 ◽

2021 ◽

Author(s):

Hitoshi Kawasuji ◽

Yoshitomo Morinaga ◽

Hideki Tani ◽

Yumiko Saga ◽

Makito Kaneda ◽

...

Keyword(s):

Age Groups ◽

Older Age ◽

Spike Protein ◽

Wild Type Virus ◽

Type Virus ◽

Wild Type ◽

Neutralizing Activity ◽

Age Dependent ◽

Induced Immunity

Since mRNA vaccines utilize wild-type SARS-CoV-2 spike protein as an antigen, there are potential concerns about acquiring immunity to variants of this virus. The neutralizing activity in BNT162b2-vaccinated individuals was higher against the wild-type virus than against its variants; this effect was more apparent in older age groups.

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A Novel T608R Missense Mutation in Insulin Receptor Substrate-1 Identified in a Subject with Type 2 Diabetes Impairs Metabolic Insulin Signaling

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/jc.2002-020933 ◽

2003 ◽

Vol 88 (4) ◽

pp. 1468-1475 ◽

Cited By ~ 31

Author(s):

Diana L. Esposito ◽

Yunhua Li ◽

Cinzia Vanni ◽

Sandra Mammarella ◽

Serena Veschi ◽

...

Keyword(s):

Type 2 Diabetes ◽

Insulin Receptor ◽

Insulin Signaling ◽

Kinase Activity ◽

Kinase Assay ◽

Insulin Receptor Substrate ◽

Wild Type ◽

Insulin Receptor Substrate 1 ◽

Naturally Occurring

Naturally occurring mutations in insulin receptor substrate-1 (IRS-1) have previously been implicated in impaired insulin action. We now report a novel mutation in IRS-1 with substitution of Arg for Thr608 that was identified in a patient with type 2 diabetes mellitus. We detected the T608R mutation in 1 of 136 chromosomes from diabetic patients and in 0 of 120 chromosomes from nondiabetic controls, suggesting that this is a rare IRS-1 variant. Conservation of Thr608 in human, monkey, rat, mouse, and chicken IRS-1 sequences is consistent with a crucial function for this residue. Moreover, Thr608 is located near the YMXM motif containing Tyr612 that is important for binding and activation of phosphoinositol 3-kinase (PI 3-kinase). To investigate whether the T608R mutation impairs insulin signaling, we transiently transfected NIH-3T3IR cells with hemagglutinin-tagged wild-type or T608R mutant IRS-1 constructs. Recombinant IRS-1 immunoprecipitated from transfected cells treated with or without insulin was subjected to immunoblotting for the p85 regulatory subunit of PI 3-kinase as well as a PI 3-kinase assay. As expected, in control cells transfected with wild-type IRS-1, insulin stimulation caused an increase in p85 coimmunoprecipitated with IRS-1 as well as a 10-fold increase in IRS-1-associated PI 3-kinase activity. Interestingly, when cells transfected with IRS1-T608R were stimulated with insulin, both the amount of p85 coimmunoprecipitated with IRS1-T608R as well as the associated PI 3-kinase activity were approximately 50% less than those observed with wild-type IRS-1. Moreover, in rat adipose cells, overexpression of IRS1-T608R resulted in significantly less translocation of GLUT4 to the cell surface than comparable overexpression of wild-type IRS-1. We conclude that a naturally occurring substitution of Arg for Thr608 in IRS-1 is a rare human mutation that may contribute to insulin resistance by impairing metabolic signaling through PI 3-kinase-dependent pathways.

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Characterization of the wild-type form of 4a-carbinolamine dehydratase and two naturally occurring mutants associated with hyperphenylalaninemia.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.92.26.12384 ◽

1995 ◽

Vol 92 (26) ◽

pp. 12384-12388 ◽

Cited By ~ 13

Author(s):

G. Johnen ◽

D. Kowlessur ◽

B. A. Citron ◽

S. Kaufman

Keyword(s):

Wild Type ◽

Naturally Occurring ◽

Type Form ◽

Wild Type Form

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The effect of salt on the dynamics of CoV-2 RBD at ACE2

10.1101/2020.10.09.333948 ◽

2020 ◽

Author(s):

E. K. Peter ◽

A. Schug

Keyword(s):

Viral Entry ◽

Membrane Surface ◽

Direct Interaction ◽

Human Cells ◽

Spike Protein ◽

Terminal Part ◽

Binding Interface ◽

Strong Binding ◽

Protein Receptor

ABSTRACTIn this article, we investigate the effect of electrolytes on the stability of the complex between the coronavirus type 2 spike protein receptor domain (CoV-2 RBD) and ACE2, which plays an important role in the activation cascade at the viral entry of CoV-2 into human cells. At the cellular surface, electrolytes play an important role, especially in the interaction of proteins near the membrane surface. Additionally, the binding interface of the CoV-2 RBD - ACE2 complex is highly hydrophilic. We simulated the CoV-2 RBD - ACE2 complex at varying salt concentrations over the concentration range from 0.03 M to 0.3 M of calcium and sodium chloride over an individual simulation length of 750 ns in 9 independent simulations (6.75 µs total). We observe that the CoV-2 RBD - ACE2 complex is stabilized independent of the salt concentration. We identify a strong negative electrostatic potential at the N-terminal part of CoV-2 RBD and we find that CoV-2 RBD binds even stronger at higher salt concentrations. We observe that the dynamics of the N-terminal part of CoV-2 RBD stabilize the protein complex leading to strong collective motions and a stable interface between CoV-2 RBD and ACE2. We state that the sequence of CoV-2 RBD might be optimized for a strong binding to ACE2 at varying salt concentrations at the cellular surface, which acts as a key component in the activation of CoV-2 for its viral entry.SIGNIFICANCEA novel coronavirus, coronavirus type 2 (CoV-2), was identified as primary cause for a worldwide pandemic of the severe acute respiratory syndrome (SARS CoV-2). The CoV-2 spike protein is a major target for the development of a vaccine and potential strategies to inhibit the viral entry into human cells. At the cellular surface, CoV-2 activation involves the direct interaction between ACE2 and CoV-2 RBD. At the cellular surface, electrolytes play an important role, especially in the interaction of proteins near the membrane surface. We thus investigate the effect of ion conditions on the interaction of the CoV-2 RBD - ACE2 complex and find stabilizing effects. We speculate that CoV-2 RBD is optimized for strong binding to ACE2 at varying salt concentrations.

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Evaluation of flow-cytometry for the monitoring of infectious human rotavirus in water

Water Science & Technology ◽

10.2166/wst.1997.0776 ◽

1997 ◽

Vol 35 (11-12) ◽

pp. 451-453

Author(s):

F. X. Abad ◽

A. Bosch ◽

J. Comas ◽

D. Villalba ◽

R. M. Pintó

Keyword(s):

Flow Cytometry ◽

Water Samples ◽

Wild Type ◽

Cell Monolayers ◽

Naturally Occurring ◽

Human Rotavirus ◽

Faecal Samples

A method has been developed for the detection of infectious human rotavirus (HRV), based on infection of MA104 and CaCo-2 cell monolayers and ulterior flow cytometry. The sensitivity of the flow cytometry procedure for the cell-adapted HRV enabled the detection of 200 and 2 MPNCU in MA104 and CaCo-2 cells, respectively. Flow cytometry performed five days after infection of CaCo-2 enabled the detection of naturally occurring wild-type HRV in faecal samples and concentrated water samples.

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Scorpion toxin-potassium channel interaction law and its applications.

Venoms and Toxins ◽

10.2174/2666121701999200531143349 ◽

2020 ◽

Vol 01 ◽

Author(s):

Zheng Zuo ◽

Zongyun Chen ◽

Zhijian Cao ◽

Wenxin Li ◽

Yingliang Wu

Keyword(s):

Potassium Channel ◽

Scorpion Toxin ◽

Scorpion Toxins ◽

Toxin Binding ◽

Channel Interaction ◽

Binding Interface ◽

Α Helix ◽

Interaction Law ◽

Binding Interfaces ◽

Β Sheet

: The scorpion toxins are the largest potassium channel-blocking peptide family. The understanding of toxin binding interfaces is usually restricted by two classical binding interfaces: one is the toxin α-helix motif, the other is the antiparallel β-sheet motif. In this review, such traditional knowledge was updated by another two different binding interfaces: one is BmKTX toxin using the turn motif between the α-helix and antiparallel β-sheet domains as the binding interface, the other is Ts toxin using turn motif between the β-sheet in the N-terminal and α-helix domains as the binding interface. Their interaction analysis indicated that the scarce negatively charged residues in the scorpion toxins played a critical role in orientating the toxin binding interface. In view of the toxin negatively charged amino acids as “binding interface regulator”, the law of scorpion toxin-potassium channel interaction was proposed, that is, the polymorphism of negatively charged residue distribution determines the diversity of toxin binding interfaces. Such law was used to develop scorpion toxin-potassium channel recognition control technique. According to this technique, three Kv1.3 channel-targeted peptides, using BmKTX as the template, were designed with the distinct binding interfaces from that of BmKTX through modulating the distribution of toxin negatively charged residues. In view of the potassium channel as the common targets of different animal toxins, the proposed law was also shown to helpfully orientate the binding interfaces of other animal toxins. Clearly, the toxin-potassium channel interaction law would strongly accelerate the research and development of different potassium channelblocking animal toxins in the future.

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Semi-Synthesis of Small Molecules of Aminocarbazoles: Tumor Growth Inhibition and Potential Impact on p53

Molecules ◽

10.3390/molecules26061637 ◽

2021 ◽

Vol 26 (6) ◽

pp. 1637

Author(s):

Solida Long ◽

Joana B. Loureiro ◽

Carla Carvalho ◽

Luís Gales ◽

Lucília Saraiva ◽

...

Keyword(s):

Growth Inhibition ◽

Small Molecules ◽

Tumor Cells ◽

Mutant P53 ◽

Wild Type ◽

Naturally Occurring ◽

Growth Inhibitory ◽

Growth Inhibitory Activity ◽

Amino Derivatives ◽

Carbazole Alkaloids

The tumor suppressor p53 is inactivated by mutation in approximately 50% of human cancers. Small molecules that bind and stabilize those mutants may represent effective anticancer drugs. Herein, we report the tumor cell growth inhibitory activity of carbazole alkaloids and amino derivatives, as well as their potential activation of p53. Twelve aminocarbazole alkaloids were semi-synthesized from heptaphylline (1), 7-methoxy heptaphylline (2), and 7-methoxymukonal (3), isolated from Clausena harmandiana, using a reductive amination protocol. Naturally-occurring carbazoles 1–3 and their amino derivatives were evaluated for their potential effect on wild-type and mutant p53 activity using a yeast screening assay and on human tumor cell lines. Naturally-occurring carbazoles 1–3 showed the most potent growth inhibitory effects on wild-type p53-expressing cells, being heptaphylline (1) the most promising in all the investigated cell lines. However, compound 1 also showed growth inhibition against non-tumor cells. Conversely, semi-synthetic aminocarbazole 1d showed an interesting growth inhibitory activity in tumor cells expressing both wild-type and mutant p53, exhibiting low growth inhibition on non-tumor cells. The yeast assay showed a potential reactivation of mutant p53 by heptaphylline derivatives, including compound 1d. The results obtained indicate that carbazole alkaloids may represent a promising starting point to search for new mutp53-reactivating agents with promising applications in cancer therapy.

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Responsiveness to exogenous cAMP of a Saccharomyces cerevisiae strain conferred by naturally occurring alleles of PDE1 and PDE2.

Genetics ◽

10.1093/genetics/135.2.321 ◽

1993 ◽

Vol 135 (2) ◽

pp. 321-326 ◽

Cited By ~ 2

Author(s):

H Mitsuzawa

Keyword(s):

Saccharomyces Cerevisiae ◽

Slow Growth ◽

Loss Of Function ◽

Wild Type ◽

Triple Mutant ◽

Apparent Absence ◽

Camp Pathway ◽

Naturally Occurring ◽

Elevated Activity ◽

Growth Phenotype

Abstract The Saccharomyces cerevisiae strain P-28-24C, from which cAMP requiring mutants derived, responded to exogenously added cAMP. Upon the addition of cAMP, this strain showed phenotypes shared by mutants with elevated activity of the cAMP pathway. Genetic analysis involving serial crosses of this strain to a strain with another genetic background revealed that the responsiveness to cAMP results from naturally occurring loss-of-function alleles of PDE1 and PDE2, which encode low and high affinity cAMP phosphodiesterases, respectively. In addition, P-28-24C was found to carry a mutation conferring slow growth that lies in CYR1, which encodes adenylate cyclase, and the slow growth phenotype caused by the cyr1 mutation was suppressed by the pde2 mutation. Therefore P-28-24C is fortuitously a pde1 pde2 cyr1 triple mutant. Responsiveness to cAMP conferred by pde mutations suggests that S. cerevisiae cells are permeable to cAMP to some extent and that the apparent absence of effect of exogenously added cAMP on wild-type cells is due to immediate degradation by cAMP phosphodiesterases.

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Discovery of natural product ovalicin sensitive type 1 methionine aminopeptidases: molecular and structural basis

Biochemical Journal ◽

10.1042/bcj20180874 ◽

2019 ◽

Vol 476 (6) ◽

pp. 991-1003 ◽

Cited By ~ 1

Author(s):

Vijaykumar Pillalamarri ◽

Tarun Arya ◽

Neshatul Haque ◽

Sandeep Chowdary Bala ◽

Anil Kumar Marapaka ◽

...

Keyword(s):

Natural Product ◽

Active Site ◽

Covalent Modification ◽

Structural Basis ◽

Wild Type ◽

Methionine Aminopeptidases ◽

Synthetic Derivative ◽

Dynamics Simulations

Abstract Natural product ovalicin and its synthetic derivative TNP-470 have been extensively studied for their antiangiogenic property, and the later reached phase 3 clinical trials. They covalently modify the conserved histidine in Type 2 methionine aminopeptidases (MetAPs) at nanomolar concentrations. Even though a similar mechanism is possible in Type 1 human MetAP, it is inhibited only at millimolar concentration. In this study, we have discovered two Type 1 wild-type MetAPs (Streptococcus pneumoniae and Enterococcus faecalis) that are inhibited at low micromolar to nanomolar concentrations and established the molecular mechanism. F309 in the active site of Type 1 human MetAP (HsMetAP1b) seems to be the key to the resistance, while newly identified ovalicin sensitive Type 1 MetAPs have a methionine or isoleucine at this position. Type 2 human MetAP (HsMetAP2) also has isoleucine (I338) in the analogous position. Ovalicin inhibited F309M and F309I mutants of human MetAP1b at low micromolar concentration. Molecular dynamics simulations suggest that ovalicin is not stably placed in the active site of wild-type MetAP1b before the covalent modification. In the case of F309M mutant and human Type 2 MetAP, molecule spends more time in the active site providing time for covalent modification.

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